Introduction to Protein

JL LO & HC Lee2000 June-July

Gene & Protein

• One gene, one protein• ..\talks\protein_3.ps

• Genotype & phenotype• ..\talks\protein_4.ps

What do proteins do?

• Everything

• Structural and Functional

• Structural– blood, muscle, bone, etc.

• Functional – metabolic, neural, reproduction

Aberrant gene > malfunction protein > disease

• 20 amino acids are coded by groups of three bases (triplets or CODONS)

• Bases are: C, T, U (instead of A), G

– 4x4x4 = 64• 3 are stop codons

• 61 code amino acids (with degeneracy)

The Genetic Code I

The Genetic Code II

The Genetic Code III

The Amino Acids

• Single and 3-letter Codes

• Aspartic Acid Asp D Glutamic Acid Glu E • Phenylanine Phe F Glycine Gly G • Alanine Ala A Cysteine Cys C • Histidine His H Isoleucine Ile I • Lysine Lys K Leucine Leu L • Methionine Met M Asparagine Asn N • Proline Pro P Glutamine Gln Q • Arginine Arg R Serine Ser S • Threonine Thr T Valine Val V• Tryptophan Trp W Tyrosine Tyr

Y

Alanine

Grey - carbon

White - hydrogen

Blue – nitrogen

Red – oxygen

Carboxylic acid group

Amine groupAlpha carbon

Side chain

The CORN Law

alpha Carbon

cabOxylic acid group

side chain (R)

amiNe group

Two AminoAcids = 2 x (CORN) – > Dipeptide + Water

(NCR) –CO2- + NH3

+ –(CRO)

= (N – C – R) – C=O

| peptide bond

H – N – (C – R – O) + H2O

Peptide Synthesis

Polypeptide – chain of peptides

Hydrophobic-Aliphatic

• Ala(A)

• Val(V)

• Leu(L)

• Ile (I)

• Mostly are bifurcated except Ala

Classification of Amino Acid Side Chains

Hydrophobic-aromatic

• Phe(F)

• Tyr(Y)

• Trp(W)

• Non-polar

Neutral-polar side chains

• Ser(S)

• Thr(T)

• Cys(C)

• Met(M)

• Asn(N)

• Gln(Q)

• Possess hydroxyl group

Acidic amino acids

• Asp(D)

• Glu(E)

• Strongly polar nature

• Catalytic

• Metal ion binding ability

Basic amino acids

• His(H)

• Lys(K)

• Arg(R)

• Frequently occurring in enzyme

Conformationally important

• Gly(G)

• Pro(P)

• G has no side chain

• P is the most rigid one

Peptide Geometry

Peptide Torsion Angles• Three main chain torsion angle• ψ N - Calpha bond• Ψ C – Calpha bond• ω C – N bond

3D structure of peptide determined if all angles given

Protein Conformation

..\talks\protein_6.ps ..\talks\protein_7.ps

Alpha-helices

..\..\proteins\1AEP_apolipophorin_III_1.gif

Beta-sheets & coils ..\..\proteins\1FSC_fasciculin_1.gif

1IBA.pdb

Structure of Alpha-Helix

Properties of the Alpha-Helix

• A pitch of 5.4 A

• Have 3.6 amino acids residues per turn

• 3.6/5.4=1.5 --- a rise per residue

• Have negative Ψandψangles

Distortion of Alpha-Helix

• Buries against the other 2nd structure

• Solvent

• 310-helix

Structure of Beta Sheet• Negative ψand Positive Ψ• Axial distance—3.5 A • Pitch – 7A

Parallel & Anti-parallel Sheets

More Examples• ..\..\proteins\1AVH_annexin_V_1.gif

• ..\..\proteins\1ERB_pl_retinol_bp_1.gif

• ..\..\proteins\1ADN_DNA_Repair_1.gif

Tertiary Structure

• ..\talks\protein_8.ps

• More cartoons of Proteins

• Go to-files

THE END